sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.830 Å
X-ray
2004-10-06
| Name: | cAMP-specific 3',5'-cyclic phosphodiesterase 4D |
|---|---|
| ID: | PDE4D_HUMAN |
| AC: | Q08499 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.1.4.53 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 7.606 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.241 | 961.875 |
| % Hydrophobic | % Polar |
|---|---|
| 56.49 | 43.51 |
| According to VolSite | |
| HET Code: | ROF |
|---|---|
| Formula: | C17H14Cl2F2N2O3 |
| Molecular weight: | 403.207 g/mol |
| DrugBank ID: | DB01656 |
| Buried Surface Area: | 67.35 % |
| Polar Surface area: | 60.45 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 22.3682 | 21.1166 | 97.3852 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| F18 | CE1 | TYR- 159 | 4.32 | 0 | Hydrophobic |
| C5 | CG | MET- 273 | 3.95 | 0 | Hydrophobic |
| CL26 | SD | MET- 273 | 4.12 | 0 | Hydrophobic |
| C1 | CG | MET- 273 | 4.45 | 0 | Hydrophobic |
| CL26 | CB | ASP- 318 | 3.78 | 0 | Hydrophobic |
| CL26 | CD2 | LEU- 319 | 3.36 | 0 | Hydrophobic |
| F17 | CB | ASN- 321 | 3.23 | 0 | Hydrophobic |
| F17 | CG | PRO- 322 | 3.58 | 0 | Hydrophobic |
| F17 | CE1 | TYR- 329 | 3.38 | 0 | Hydrophobic |
| F18 | CB | TRP- 332 | 3.46 | 0 | Hydrophobic |
| F18 | CB | THR- 333 | 4.14 | 0 | Hydrophobic |
| CL25 | CD1 | ILE- 336 | 4.36 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 336 | 3.74 | 0 | Hydrophobic |
| F18 | CG2 | ILE- 336 | 3.84 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 336 | 4.11 | 0 | Hydrophobic |
| C23 | SD | MET- 337 | 4.15 | 0 | Hydrophobic |
| C20 | CE2 | PHE- 340 | 4.27 | 0 | Hydrophobic |
| CL25 | CE1 | PHE- 340 | 4.29 | 0 | Hydrophobic |
| C23 | CE2 | PHE- 340 | 4.13 | 0 | Hydrophobic |
| C23 | CG | MET- 357 | 3.67 | 0 | Hydrophobic |
| C22 | CE | MET- 357 | 3.51 | 0 | Hydrophobic |
| C23 | CB | SER- 368 | 3.83 | 0 | Hydrophobic |
| O15 | NE2 | GLN- 369 | 3.15 | 134.99 | H-Bond (Protein Donor) |
| O19 | NE2 | GLN- 369 | 3.11 | 152.9 | H-Bond (Protein Donor) |
| C21 | CB | PHE- 372 | 4.18 | 0 | Hydrophobic |
| C20 | CG | PHE- 372 | 3.76 | 0 | Hydrophobic |
| F17 | CE2 | PHE- 372 | 3.74 | 0 | Hydrophobic |
| N7 | O | HOH- 2009 | 2.93 | 156.4 | H-Bond (Ligand Donor) |
